PlantSynBio: Construction of a plant chassis as a platform for biological discoveries and innovations

种植各种各样的植物作为食物、饲料或燃料，生物技术有可能提高这些植物的质量、产量和可持续性。生物技术的应用包括改善营养、增强对压力的适应能力、固碳、生物塑料/生物材料/生物产品/生物燃料的生产以及空间探索。然而，技术壁垒目前阻碍了具有复杂新功能的工厂的建设。该项目将产生一个新颖的，第一个同类平台-底盘-这将使设计和制造具有新颖特性的工厂成为可能。这些特性包括：1）高价值化学品的生产，如农药、生物材料、生物塑料和药品; 2）改善碳封存，以解决全球二氧化碳水平过高的问题; 3）增强可持续性，如减少对肥料或杀虫剂的需求; 4）提高对干旱和温度压力的弹性和适应能力。为了鼓励参与科学，并向年轻一代传达科学可以应对全球挑战，该项目将直接让本科生参与底盘的表征。为了扩大科学参与者的多样性，该项目将招募和培训新兴生物技术和计算方法方面代表性不足的群体的成员，从而帮助发展科学学科的21世纪劳动力。 在世纪，基因组学和生物技术的关系将是开发具有提高的产量、营养和市场质量、增强的对生物和非生物胁迫的适应性、增加的可持续性和/或新的表型（例如封存碳或合成生物产品、生物材料和新的自然分子的能力）的植物。为了实现农业的“第三次绿色革命”，我们需要有能力设计复杂的途径和过程，以利用植物的可持续生产平台。最小细菌和酵母基因组的发展允许基因组的重写，并提高了工程微生物在生物技术中的效用。先进的植物基因组工程方法和资源对于植物作为生物经济中的可持续平台至关重要。单一或组合工程复杂的代谢途径和发育过程的一个障碍是由于所有被子植物中的全/节段基因组和基因复制导致的基因功能的绝对冗余。该项目将开发一个大规模的基因编辑平台，该平台将用于生成具有减少的基因含量和冗余的新型植物基因型，其可以作为底盘（即，一个平台），以快速工程改造具有新表型的植物，并测试与感兴趣的生物过程相关的异源基因。这个项目将是创建一个真正的最小植物基因组的第一阶段，这样我们就可以开始重写基因组，以获得新的自然分子和生物过程。由于其身材矮小，生命周期快，易于转化，创建最小植物基因组的合理选择是拟南芥，即鼠耳水芹。我们的具体目标包括一个设计阶段和两个周期的构建-测试-学习，其中我们使用最先进的多重基因编辑方法，在跨越拟南芥基因组的18个5 Mb模块中删除324个蛋白质编码基因。将通过模块的成对和高阶杂交检测合成致死对的存在。机器学习方法将与经验和生物信息学数据一起使用，以开发和改进预测基因可分配性的模型。该项目将包括一个垂直整合项目，所有人员都参与该项目和机构，并且更多的本科生可以通过题为“构建最小植物基因组以实现可持续生物经济”的定制课程参与。该项目将使代表性不足的群体参与到与21世纪世纪相关的STEM学科中。该项目由ENG/CBET的细胞和生物化学工程项目以及BIO/MCB的系统和合成生物学项目共同支持。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

A wide range of plants are grown for food, feed or fuel, and biotechnology has the potential to improve the quality, yield, and sustainability of these plants. Biotechnology applications include improving nutrition, enhancing resilience to stress, carbon sequestration, production of bioplastics/biomaterials/bioproducts/biofuels, and space exploration. Yet, technology barriers currently prevent construction of plants with complex new features. This project will generate a novel, first-of-its-kind platform - a chassis - that will enable the design and fabrication of plants with novel properties. These properties include 1) the production of high value chemicals such as pesticides, bio-materials, bio-plastics, and pharmaceuticals, 2) improved carbon sequestration to address excess global carbon dioxide levels, 3) enhanced sustainability such as the reduced need for fertilizer or insecticides and 4) improved resiliency and adaptation to drought and temperature stress. To encourage participation in science and to convey to a younger generation that science can address global challenges, this project will directly engage undergraduates in the characterization of the chassis. To broaden the diversity of participants in science, this project will recruit and train members of under-represented groups in emerging biotechnology and computational methods, thereby aiding development of a 21st century workforce in scientific disciplines. In the 21st century, the nexus of genomics and biotechnology will be the development of plants with improved yield, nutrition, and market quality, enhanced resilience to biotic and abiotic stressors, increased sustainability, and/or novel phenotypes such as the ability to sequester carbon or synthesize bio-products, biomaterials, and new-to-nature molecules. To achieve this ‘Third Green Revolution’ in agriculture, we need the ability to engineer complex pathways and processes to harness the sustainable production platform of plants. Development of minimal bacterial and yeast genomes have permitted the rewriting of genomes and enhanced the utility of engineered microbes for biotechnology. Advancing plant genome engineering methods and resources are essential for plants to be utilized as sustainable platforms in the bioeconomy. One barrier to either singly or combinatorial engineering complex metabolic pathways and developmental processes is the sheer redundancy of gene function due to whole/segmental genome and gene duplication in all angiosperms. This project will develop a gene editing platform at scale that will be used to generate novel plant genotypes with reduced gene content and redundancy, which can serve as chassis (i.e., a platform) to rapidly engineer plants with new phenotypes and test heterologous genes relevant to biological processes of interest. This project will be the first phase in creating a true minimal plant genome, such that we can begin to rewrite the genome for new-to-nature molecules and biological processes. Due to its small stature, rapid life cycle, and amenability to transformation, the logical choice for creating a minimal plant genome is Arabidopsis thaliana, the mouse-ear cress. Our specific aims include a design phase and two cycles of build-test-learn in which we target 324 protein-coding genes for deletion across 18 5 Mb modules that span the Arabidopsis genome using state-of-the-art multiplexed gene editing approaches. The presence of synthetic lethal pairs will be tested through pairwise and higher order crosses of the modules. Machine learning approaches will be used with empirical and bioinformatic data to develop and improve models that predict gene dispensability. This project will include a Vertically Integrated Project in which all personnel are engaged across the project and institutions and in which a larger number of undergraduates can participate via a custom course entitled Building a Minimal Plant Genome to Enable a Sustainable Bioeconomy. This project will engage under-represented groups to advance participation in STEM disciplines relevant for the 21st century.This project is jointly supported by the Cellular and Biochemical Engineering Program in ENG/CBET, and the Systems and Synthetic Biology Program in BIO/MCB.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.